NationalGenomicsInfrastructure/piper

Issues

• FixEmptyReads.pl not bundled in Piper 1.4.0

  #82 opened 6 years ago by johanherman
  0

• Support compressing vcf files

  #66 opened 9 years ago by b97pla
  0

• Coverage not correct

  #49 opened 10 years ago by parlundin
  3

• calculate checksums for the produced files

  #67 opened 9 years ago by b97pla
  1

• Ordering error in setup file creation

  #64 opened 10 years ago by johandahlberg
  0

• Update VQSR parameters

  #47 opened 10 years ago by johandahlberg
  0

• Update bwa

  #53 opened 10 years ago by johandahlberg
  0

• Error in README

  #55 opened 10 years ago by jessieno
  0

• Question: is it intentional to leave out minimumBaseQuality from HaplotypeCallerBase?

  #59 opened 10 years ago by biocyberman
  1

• Spelling error: sequenceingcenter -> sequencingcenter

  #62 opened 10 years ago by johandahlberg
  0

• Not enough memory, better way to determine Xmx value

  #63 opened 10 years ago by biocyberman
  5

• Piper failed for a sample with a name that looks like '3-NOP'

  #54 opened 10 years ago by jessieno
  0

• Generate snpEff html

  #61 opened 10 years ago by parlundin
  0

• SnpEff ends up in wrong place in dependency graph for exome runs

  #60 opened 10 years ago by johandahlberg
  0

• Maybe a bug: Qualimap step does not detect failure

  #58 opened 10 years ago by biocyberman
  1

• Question: How to rerun from a particular analysis step?

  #56 opened 10 years ago by biocyberman
  2

• Less memory for samtools sort

  #48 opened 10 years ago by johandahlberg
  3

• Incorrect paths for index and reference files when running RNAcounts workflow

  #57 opened 10 years ago by jessieno
  0

• Picard metrics file deleted

  #41 opened 10 years ago by ewels
  4

• UPPMAX: Memory overflow error

  #36 opened 10 years ago by parlundin
  4

• Add snpEff

  #43 opened 10 years ago by ewels
  22

• Bug: Can't detect 'path' not set for a resource or program

  #50 opened 10 years ago by biocyberman
  2

• Change default path to resource file to ua-sthlm communal project

  #34 opened 10 years ago by johandahlberg
  0

• Qualimap: add parameter for comparing GC content distribution with the reference

  #37 opened 10 years ago by ewels
  1

• Upgrade to Qualimap 2.0

  #44 opened 10 years ago by parlundin
  4

• Update to GATK 3.3

  #46 opened 10 years ago by johandahlberg
  0

• setupFileCreator return code is 0 even if it fails

  #35 opened 10 years ago by mariogiov
  3

• .done file generated but its not done

  #38 opened 10 years ago by parlundin
  4

• Some questions before adoption of piper

  #45 opened 10 years ago by biocyberman
  3

• FastQC added into Piper

  #29 opened 10 years ago by johandahlberg
  2

• Question for the man

  #42 opened 10 years ago by mariogiov
  2

• Just one sample in delivery folder when running multiple samples

  #40 opened 10 years ago by parlundin
  3

• Genotype concordance error

  #39 opened 10 years ago by mariogiov
  1

• Add concordance check with snp-genotyping

  #27 opened 10 years ago by johandahlberg
  3

• Commandline option in setupFileCreator to specify qos is missing

  #33 opened 10 years ago by johandahlberg
  0

• setupFileCreator regex bug

  #31 opened 10 years ago by mariogiov
  1

• Haloplex script needs update to new way of fetching resources

  #32 opened 10 years ago by johandahlberg
  0

• Report of versions

  #23 opened 10 years ago by jessieno
  2

• Change the pipeline setup xml to some more "flexible" solution

  #28 opened 10 years ago by johandahlberg
  8

• fc_id naming convention and stckh2UUSNPSEQ

  #26 opened 10 years ago by vezzi
  1

• Piper return code

  #30 opened 10 years ago by vezzi
  4

• sthlm2UUSNP NoClassDefFound

  #25 opened 10 years ago by mariogiov
  3

• sthlm2UUSNP problem on M.Kaller

  #22 opened 10 years ago by vezzi
  17

• Running piper on M.Kaller_14_06

  #21 opened 10 years ago by vezzi
  7

• SetupFileCreator problem

  #18 opened 10 years ago by vezzi
  5

• Fall back to copying instead of hard linking

  #24 opened 10 years ago by johandahlberg
  0

• sthlm2UUSNP problem with dual-indexing

  #20 opened 10 years ago by vezzi
  2

• Update to GATK version 3.2-2

  #19 opened 10 years ago by johandahlberg
  1

• sthlm2UUSNP and four-tier directory format

  #17 opened 10 years ago by mariogiov
  12

• Qualimap fails

  #16 opened 10 years ago by vezzi
  3